The mechanisms of humic substances self-assembly with biological molecules: The case study of the prion protein

Humic Substances as a Versatile Intermediary

Humic substances are organic ubiquitous components arising in the process of chemical and microbiological oxidation, generally called humification, the second largest process of the carbon cycle. The beneficial properties of these various substances can be observed in many fields of life and health, whether it is the impact on the human organism, as prophylactic as well as the therapeutic effects; animal physiology and welfare, which is widely used in livestock farming; or the impact of humic substances on the environment and ecosystem in the context of renewal, fertilization and detoxification. Since animal health, human health and environmental health are interconnected and mutually influencing, this work brings insight into the excellence of the use of humic substances as a versatile mediator contributing to the promotion of One Health.

Formation and nature of non-extractable residues of emerging organic contaminants in humic acids catalyzed by laccase

Formation of non-extractable residues (NERs) is the major fate of most environmental organic contaminants in soil, however, there is no direct evidence yet to support the assumed physical entrapment of NERs (i.e., type I NERs) inside soil humic substances. Here, we used ¹⁴C-radiotracer and silylation techniques to analyze NERs of six emerging and traditional organic contaminants formed in a suspension of humic acids (HA) under catalysis of the oxidative enzyme laccase. Laccase induced formation of both type I and covalently bound NERs (i.e., type II NERs) of bisphenol A, bisphenol F, and tetrabromobisphenol A to a large extent, and of bisphenol S (BPS) and sulfamethoxazole (SMX) to a less extent, while no induction for phenanthrene. The type I NERs were formed supposedly owing to laccase-induced alteration of primary (active groups) and secondary (conformation) structure of humic supramolecules, contributing surprisingly to large extents (23.5%-65.7%) to the total NERs, particularly for BPS and SMX, which both were otherwise not transformed by laccase catalysis. Electron-withdrawing sulfonyl group and bromine substitution significantly decreased amount and kinetics of NER formation, respectively. This study provides the first direct evidence for the formation of type I NERs in humic substances and implies a "Trojan horse" effect of such NERs in the environment.

The Effect of Supramolecular Humic Acids on the Diffusivity of Metal Ions in Agarose Hydrogel

Humic acids are known as natural substances of a supramolecular nature. Their self-assembly ability can affect the migration of heavy metals and other pollutants in nature. The formation of metal-humic complexes can decrease their mobility and bioavailability. This study focuses on metal ions diffusion and immobilization in humic hydrogels. Humic acids were purchased from International Humic Substances Society (isolated from different matrices—peat, soil, leonardite, water) and extracted from lignite mined in Czech Republic. Copper(II) ions were chosen as a model example of reactive metals for the diffusion experiments. The model of instantaneous planar source was used for experimental data obtained from monitoring the time development of copper(II) ions distribution in hydrogel. The effective diffusion coefficients of copper(II) ions showed the significant dependence on reaction ability of humic hydrogels. Lower amounts of the acidic functional groups caused an increase in the effective diffusion coefficient. In general, diffusion experiments seem to act as a valuable method for reactivity mapping studies on humic substances.

Conformational modifications of lysozyme caused by interaction with humic acid studied with spectroscopy

Modification of enzyme/protein conformation will affect the activities and functionality of enzymes. Previous studies have shown that the activity of lysozyme (LSZ) in the presence of humic acid (HA) is largely determined by the mass ratio of HA/LSZ (f = mHA/mLSZ), pH and ionic strength. Here the interaction and conformation of LSZ in HA/LSZ-complex/aggregate (HA/LSZ-c/a) were investigated by spectroscopic techniques at (initial) pH 5 and 8 and ionic strength 5 mmol/L. The results indicated a strong interaction between HA and LSZ. Circular dichroism (CD), and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy showed that the helix content reached a minimum at the mass ratio of its iso electric point (IEP) at given initial pH, f_IEP,pHi. The changes in β-sheet and random coil of HA/LSZ-c/a were opposite with increasing f. The minimum of helix content at f_IEP,pHi corresponded with the minimum LSZ activity and maximum aggregate size of HA/LSZ-c/a. UV-vis spectra and fluorescence measurements indicated that the amino acid residues (especially for tyrosine) in LSZ were in a more hydrophobic microenvironment before f_IEP,pHi due to the formation of HA/LSZ-c/a, while were gradually exposed to a more polar microenvironment beyond f_IEP,pHi with the disaggregation of HA/LSZ-c/a. HA and LSZ interaction caused a more hydrophobic microenvironment for the amino acid residues at initial pH 8. This study improves our understanding of enzyme/protein behavior in the natural environment.

Exploring the structure and dynamics of proteins in soil organic matter

Alongside inorganic materials, water, and air, soil organic matter (SOM) is one of the major components of soil and has tremendous influence on the environment given its vital role in the carbon cycle. Many soil dwelling organisms like plants, fungi and bacteria excrete proteins, whose interaction with SOM is poorly understood on an atomistic level. In this study, molecular dynamics simulations were used to investigate selected proteins in soil models of different complexity from simple co-solvent molecules to Leonardite humic acids (LHA). We analyzed the proteins in terms of their structural stability, the nature and strength of the interactions with their surroundings, as well as their aggregation behavior. Upon insertion of proteins in complex SOM models, their structural stability decreased, although no unfolding or disruption of secondary structure was observed. The interactions of proteins and SOM were primarily governed by electrostatic forces, often in form of hydrogen bonds. However, also weaker van der Waals forces made a significant contribution to the total interaction energies. Moreover, we showed that even though the molecular structure and size of SOM molecules varied, the functional groups of SOM ordered around the protein in a similar pattern. Finally, the number of aggregates formed by proteins and SOM molecules was shown to be primarily proportional to the size of the latter. Strikingly, for varying protein net charges no changes in the formation of aggregates with the strongly negatively charged LHA were observed.

How Humic Acids Affect the Rheological and Transport Properties of Hydrogels

Humic acids are often regarded as substances with a supramolecular structure which plays an important role in Nature. Their addition into hydrogels can affect their behavior and functioning in different applications. This work is focused on the properties of widely-used hydrogel based on agarose after addition of humic acids-the protonated H-form of humic acids and humic acids with methylated carboxylic groups. Hydrogels enriched by humic acids were studied in terms of their viscoelastic and transport properties. Rotational rheometry and methods employing diffusion cells were used in order to describe the influence of humic acids on the properties and behavior of hydrogels. From the point of view of rheology the addition of humic acids mainly affected the loss modulus corresponding to the relaxation of hydrogel connected with its flow. In the case of diffusion experiments, the transport of dyes (methylene blue and rhodamine) and metal ions (copper and nickel) through the hydrogel was affected by interactions between humic acids and the diffusion probes. The time lag in the hydrogel enriched by humic acids was prolonged for copper, methylene blue and rhodamine. In contrast, the presence of humic acids in hydrogel slightly increased the mobility of nickel. The strongest influence of the methylation of humic acids on diffusion was observed for methylene blue.

Soil humic acids degrade CWD prions and reduce infectivity

Chronic wasting disease (CWD), an environmentally transmissible, fatal prion disease is endemic in North America, present in South Korea and has recently been confirmed in northern Europe. The expanding geographic range of this contagious disease of free-ranging deer, moose, elk and reindeer has resulted in increasing levels of prion infectivity in the environment. Soils are involved in CWD horizontal transmission, acting as an environmental reservoir, and soil mineral and organic compounds have the ability to bind prions. Upper horizons of soils are usually enriched with soil organic matter (SOM), however, the role of SOM in prion conservation and mobility remains unclear. In this study, we show that incubation of PrP^CWD with humic acids (HA), a major SOM compound, affects both the molecular weight and recovery of PrP^CWD. Detection of PrP^CWD is reduced as HA concentration increases. Native HA extracted from pristine soils also reduces or entirely eliminates PrP^CWD signal. Incubation of CWD prions with HA significantly increased incubation periods in tgElk mice demonstrating that HA can reduce CWD infectivity.

Chronic wasting disease (CWD) is a contagious prion disease affecting several species of captive and wild cervids. Environmental prion contamination plays a major role in increasing incidence of CWD, with CWD infectivity being released into the environment by decaying carcasses, or shedding of biological fluids including urine, feces, and saliva. Horizontal transmission of CWD involves soils as an environmental reservoir of infectivity. Here, we tested the role of a soil organic matter compound, humic acid, for its ability to bind CWD prions and impact infectivity. A wide range of humic acid concentrations were examined representing the extensive spectrum of humic acid levels present in native soils. We found that incubation of CWD prions with high concentrations of humic acids (>2.5 g L^-1) decreases the both CWD-prion signal and infectivity, whereas lower levels of humic acids did not significantly impact protein stability or infectivity. Our study provides new insights into soil-prion interactions, prions persistence in soil, and their bioavailability to grazing animals.